{"doi":"10.1261/rna.080188.124","title":"Improved functions for nonlinear sequence comparison using SEEKR","abstract":"SEquence Evaluation through k -mer Representation (SEEKR) is a method of sequence comparison that uses sequence substrings called k -mers to quantify the nonlinear similarity between nucleic acid species. We describe the development of new functions within SEEKR that enable end-users to estimate P- values that ascribe statistical significance to SEEKR-derived similarities, as well as visualize different aspects of k -mer similarity. We apply the new functions to identify chromatin-enriched lncRNAs that contain XIST -like sequence features, and we demonstrate the utility of applying SEEKR on lncRNA fragments to identify potential RNA-protein interaction domains. We also highlight ways in which SEEKR can be applied to augment studies of lncRNA conservation, and we outline the best practice of visualizing RNA-seq read density to evaluate support for lncRNA annotations before their in-depth study in cell types of interest.","journal":"RNA","year":2024,"id":458249,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":5,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9524,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":991693,"name":"Quinn E. Eberhard","orcid":"0000-0003-4197-1703","position":1,"is_corresponding":false},{"id":1284555,"name":"Luke Ni","orcid":null,"position":2,"is_corresponding":false},{"id":275050,"name":"J. Mauro Calabrese","orcid":"0000-0002-1213-2540","position":3,"is_corresponding":false},{"id":331909,"name":"Shuang Li","orcid":"0000-0003-4658-9765","position":0,"is_corresponding":true}],"reference_count":41,"raw_metadata":null,"created_at":"2026-07-19T02:03:46.117860Z","pmid":"39187382","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}